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Protists and their plastids

A quick skim through this blog reveals fairly quickly that I have a slight fixation on bacteria. I like to research them, read about them, and then blog about them, most specifically about their cell walls. However life contains more than just bacteria, and occasionally, strange though it might seem, people write papers about such non-bacterial things, and they end up on my desk with a small post-it attached reminding me that I have a presentation for my supervision group coming up.

So for the sake of my supervision, and to prevent myself becoming too scientifically blinkered, I took a quick foray this weekend into the murky world of protists, the strange and wonderful organisms that occupy the taxonomic equivalent of the 'misc.' draw in a filing cabinet. The creatures that are neither plant, nor animal, nor demonstrably bacteria. Many of them are single celled, some of them photosynthesise, and they all seem to occupy little evolved niches of their own, producing proteins with no noticeable homologues in any other branch of life.

The paper has the rather terrifying title of : "Rampant polyuridylylation of plastid gene transcripts in the dinoflagellate Lingulodinium". And I am not ashamed to admit that I had to go double-check the meaning of several of those words.

Dinoflagellates are little organisms that live in water, and mostly look a little like the picture on the right. Many of them are marine organisms, making up a large amount of the photosynthesising biomass in the ocean, and occasionally blooming to form 'red tides', leading to whole sweeps of water turning bright red (possibly occasionally on biblical command). The photosynthetic ones contain chloroplasts, which are wrapped up in three membranes, rather than the usual two. These, like all chloroplasts, contain their own genetic material (known as plastid genes), although unlike plant plastids, they don't seem to contain very many, and those that they do posess are found on little minicircles.

What the paper is interested in is whether there are any other genes in the chloroplast which aren't in minicircle form. There are, afterall, only 12 genes encoded on the minicircles, which is a small amount for a plastid. In order to explore this, it uses a characteristic property of the dinflagellate species it's working with. All organisms, when making proteins, make them from an mRNA copy of the genetic code. This mRNA copy tends to have a long string of adenosine residues added to the end, in order to prevent the mRNA getting degraded. This happens in our dinoflagellate species as well, but it doesn't happen to the plastid genes.

However instead of getting multiple adenosine repeats the plastid genes get multiple uracil repeats. It's just a different base, but it allows the mRNA made in the nucleus, and the mRNA made by the chloroplast to be separated. You can probe for adenosine enriched and adenosine depleted mRNA as shown on the gel below (A and B show different species). The psbA mRNA is clearly strongly present A+ (adenosine enriched) and therefore codes for a nuclear encoded protein. Conversely, the 23S RNA is A- (adenosine depleted) and is coded for in the chloroplast, from a plastid gene.

(Image taken from reference below)

The paper selected 300 random poly-uridine mRNAs (A-) and sequenced them to see if they corresponded to genes found in minicircles, or whether they might be plastid genes held in some different architecture. All the A- mRNA corresponded to the 12 genes discovered in the minicircle. They carried out rarefaction analysis to see if their sample size was large enough, apparently it was, in fact 300 clones was way in excess of the amount needed to find a further, non-minicircled-gene.

This suggests that minicircles are the only architecture for plastid genes and, importantly, that there really are only 12 genes contained in the chloroplast of the dinoflagellate Lingulodinium. This is a very small number of genes, all the rest have somehow migrated to the nucleus, leaving these 12 behind. And it's still very much an open question about why these have been left behind. The paper, in its discussion section puts forward the possibility of size. The genes that have been left behind all code for some of the longer proteins usually found in chloroplasts, although the paper does have the good grace to admit that that's not the most convincing of arguments.

2 comments:

Dino genomes, all three of them in photosynthetic species, are ON CRACK. The plastids have minicircles (not to be confused with trypanosome kDNA minicircles - now THAT genome is severely screwed up!). The nuclear genome attaches the 5' cap via trans-splicing of "splice leaders" to every single gene produced; and is also >10x the size of the human genome, in terms of base pairs. It also lacks a couple histones, and the chromatin organisation is distinctively WEIRD.

The dino mitochondrial genomes are also *gasp* weird - linear chromosomes containing various permutations of recurring pieces of 2-3 genes and rDNA - the rDNA is scattered all over the place and has to be trans-spliced together; so are the 2-3 essential genes as well, if I recall. Furthermore, in some species there's also RNA editing!

Afterward, the dinos went on to tertiary endosymbiosis, resulting in some organisms with a massive endosymbiont seemingly competing to take it over (Kryptoperidinium), or plastid-targeting genes from two organisms sitting mashed up in one nuclear genome... (Karenia, Karlodinium).

Also, some of them (Warnowiid dinos) have...camera eyes. With image-forming lenses, retinas, and all the rest. They're unicellular. No brains, no neural tissue. Yeah. Weird.

It is my solid faith that the intelligent designer took a few hits of LSD on the 7th day, and created the protists. True story.

I am beginning to come across some weird shit in the prokaryotic kingdoms though! Sadly, all our microbiol classes are medically-inclined, so I have to learn about bacteria on my own time. This results in a slight problem that my introduction to bacterial diversity seems to come from Cavalier-Smith's papers... >_>

Thanks so much for your reply! I'm only just begining to realise how crazy protists are in terms of genome organisation (mostly through your blog to be honest), and it's totally fascinating. We never really covered protists, only a couple of random plantscis/biochemists work on them here and they don't seem to lecture.

I'm going to have to look up that competing endosymbiont though, that sounds amazing :D